Table 1 Performance of four metagenomic classifiers (BugSeq, MetaMaps, Centrifuge, and CDKAM) on GridION ZymoBIOMICS Mock Log and Even communities
From: BugSeq: a highly accurate cloud platform for long-read metagenomic analyses
Dataset used | F1 score at species level | Precision at species level (%) | Recall at species level (%) | Number of unique species detected (true count = 10) | Run time (wall clock) (hh:mm) | Classification memory requirement (GB) | Indexing time (wall clock) (hh:mm) | Indexing memory requirement (GB) | |
|---|---|---|---|---|---|---|---|---|---|
BugSeq | Even | 0.95 | 99.82 | 90.36 | 117 | 4:09 | 118 | 1:15 | 243 |
Log | 0.95 | 100 | 90.88 | 52 | 4:25 | 113 | |||
MetaMaps (miniSeq + H) | Even | 0.89 | 99.13 | 80.71 | 2144 | 86:20 | 172.6 | Prebuilt | Prebuilt |
Log | 0.94 | 99.46 | 88.25 | 1386 | 125:22 | 184.0 | |||
MetaMaps (RefSeq) | Even | Out of memory | NA | NA | |||||
Log | 0.94 | 99.73 | 88.66 | 2094 | 154:29 | 270 | |||
Centrifuge – 16 bp minimum hit length, -k 1 | Even | 0.79 | 93.00 | 69.17 | 4337 | 00:19 | 67.7 | 19:45 | 168 |
Log | 0.92 | 95.93 | 89.07 | 5777 | 00:19 | 64.4 | |||
Centrifuge – default (22 bp) minimum hit length, -k 1 | Even | 0.80 | 94.71 | 68.53 | 5380 | 00:16 | 56.9 | ||
Log | 0.93 | 97.14 | 88.65 | 5513 | 00:14 | 55.7 | |||
CDKAM (standard + human) | Even | 0.91 | 96.52 | 86.53 | 3721 | 00:09 | 34.5 | 28:23 | 66 |
Log | 0.94 | 99.06 | 89.2 | 2956 | 00:08 | 34.5 |